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HistoryNet writes:

The gesture of invoking hepatitis—especially with the scary modifier “acute,” and absent the more accurate labels of alcoholic hepatitis or alcoholic cirrhosis—spared the McCarthy family the pain of publicly acknowledging Joe’s chronic and perhaps suicidal drunkenness. A concerted cover-up seems improbable, since the Bethesda Naval medical team requested an autopsy, which Jean McCarthy vetoed.

How good is the evidence for the claim that the Bethesda Naval medical team want to perform an autopsy but that didn't happen because Jean McCarthy didn't want it to happen?

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The author of that article gives a first and therefore unique insight to this issue. Counter-facts are not available. The real cause of death was and is of quite much an issue among people close to his world-view. That indeed no autopsy was performed is widely reported in his older biographies, along with speculations about the possibilities, aside from the most popular explanation: 'drinking' -> 'liver failure'.

What we know, and what is new here:

The article on HistoryNet is written by Larry Tye and an excerpt from his recent book Larry Tye: "Demagogue: The Life and Long Shadow of Senator Joe McCarthy, Boston, Massachusetts", Houghton Mifflin Harcourt, 2020.

This book was reviewed with:

On the other hand, McCarthy had a drinking problem from an early age, and by the time he came to Washington in 1947, he was an alcoholic. The senator carried a flask of booze in his briefcase and drank heavily through the workday. Tye tells us about the drinking, but makes scant effort to explain its origins or its impact on the man or his work. His reporting shows that McCarthy must have been drunk for much of the time he was terrorizing Washington. The medical records that Tye uncovered from Bethesda Naval Hospital, where McCarthy was often treated and where he died, reveal that the drinking killed him.

— Robert G Kaiser: "Joseph McCarthy: An American demagogue who foreshadowed Trump", Washington Post, August 27, 2020.

And another review mentions a perhaps even more important detail:

While Tye’s book is hardly the last word on McCarthy, it is the first to benefit from employing the McCarthy Papers at Marquette University, closed to researchers by the fam- ily since the senator’s death in 1957. How Tye gained this access, so long sought by scholars, is unclear and unstated. But what he did with that access is superb, transforming our understanding of the senator’s life, loves, and hatreds in ways earlier historians and journalists have not been able to do.

— Gregory L. Schneider: "Review: Demagogue: The Life and Long Shadow of Senator Joe McCarthy, by Larry Tye", American Political Thought, Vol 10, No 1, Winter 2021. doi

And the author Tye references the relevant passage in his book as:

If he contracted pneumonia or some other deadly infection in their hospital, they lacked the drugs and technology we now have that might have saved him. Most likely hepatitis was just the right vanilla verdict since his liver was diseased, and pointing to that—especially with the scary-sounding adjective “acute,” and without the more accurate labels of alcoholic hepatitis or alcoholic cirrhosis—spared his family the pain of publicly acknowledging his chronic and perhaps suicidal drunkenness. A concerted cover-up seems improbable, since the Navy Hospital team requested an autopsy, which Jean refused.

— Tye Demagogue, p226.

With the accompanying endnote as:

The doctors who reviewed the hospital records were Stanley Caroff, professor of psychiatry at the University of Pennsylvania School of Medicine; Jeffrey Flier, former dean of the Harvard Medical School; Lawrence Friedman, assistant chief of medicine at Massachusetts General Hospital; and Jerome Kassirer, former editor in chief of the New England Journal of Medicine.
McCarthy’s records show that his score on the two measures used to determine the severity of alcoholic hepatitis was “just under 20,” Friedman says. “Mortality is generally associated with a value over 32.” Author interview with and emails from Friedman.
As for neuroleptic malignant syndrome, Caroff, an expert on the condition, says that while “it is theoretically possible” that the particular antipsychotics McCarthy was taking “could have worsened his temperature or caused an NMS-like reaction … there are virtually no conclusive cases published of a link.” Author interview with and emails from Caroff.

— Tye Demagogue, p337.

So, that McCarthy's true cause of death was somewhat unclear seems evident, that his drinking problems were tried to be kept hidden from public view as well. A medic wanting to know the real cause of death was a thing in pre-coronoia-times, so the desire to perform an autopsy in such a case looks plausible as well. Whether his wife indeed vetoed this undertaking cannot be answered any better from this.

Previously, this controversy was discussed as:

Joe began to take part in even fewer Senate sessions. And he began to drink more heavily. By the summer of 1956, his drinking had become so severe that he was forced to enter the Bethesda Naval Hospital for detoxification. Jean covered up for him by telling reporters he was being treated for an old knee injury he had suffered on Guadalcanal. […]

Back in Washington, McCarthy was readmitted to Bethesda Naval Hospital on April 28. At first, Jean told reporters his knee had been acting up again. A day later, she said he'd gotten a virus while in Wisconsin, and it had turned into a bad cold. In fact, his liver had begun to fail, but Jean was still trying to cover for him.

On the afternoon of May 2, 1957, McCarthy received the last rites of the Catholic Church from a priest, and that evening at 5:02, with Jean at his side, he died. He was forty-eight years old.

The death certificate gave the cause of death as "hepatitis, acute, cause unknown." Time magazine, however, reported that Joe had died of cirrhosis of the liver, a disease known to be brought on by excessive drinking. Jean, intent as always on defending him, insisted that her husband had died of hepatitis, not alcoholism, and ardent McCarthyites followed her lead.

— James Cross Giblin: "The Rise and Fall of Senator Joe McCarthy", Houghton Mifflin Harcourt: Boston, New York, 2009, p222, p233. worldcat

Likewise:

Even worse for McCarthy was what happened to his name, record, and reputation in the ensuing decades. He died on May 2, 1957, just thirty months after the censure vote, and was taken back home to Appleton to be buried on a quiet hillside by the Fox River. He was only forty-eight when he died, an incredibly young age even then for one once physically so strong, albeit with his share of ailments. Many observers thought he drank himself to death, others theorized foul play, still others that the censure and the ostracism had robbed him of the will to live.

— Medford Stanton Evans: "Blacklisted by History. The Untold Story of Senator Joe McCarthy and his Fight Against America’s Enemies", Crown Forum: New York, 2007, p338.

Note that in his father's prior book The Assasination of Joe McCarthy Medford Bryan Evans wrote (gBooks) about his belief that McCarthy could have been poisoned. By his enemies, if they had had the chance, not himself/alcohol. Although that describes more possible motivations and his popularity than actual belief of the authior. Of course, from 'could have been done' to 'was done' is just a small step in quoting the right words, out of context. A foul play version that together with 'infectious reasons' (like hepatitis) found a certain following.

The either 'critical' or perhaps even 'conspiracy theorists'' take on the matter:

There were a myriad of questions swirling around the cause of death, but as could probably be anticipated by astute researchers, no autopsy was performed. The court historians have coalesced behind the view that McCarthy was a chronic alcholic, which ignited the acute hepatitis they decided (without any conclusive evidence) killed him. […]

Since one of the few things clarified by doctors at Bethesda was the fact that McCarthy did not contract hepatitis through infection, writer Medford Evans and researcher David Martin have produced a strong argument that the disease was triggered by poison. As Medford Evans wrote in his book _The Assassination of Joe McCarthy, “I believe they would have murdered him if they could have.“

— Donald Jeffries: "Crimes And Cover-ups in American Politics: 1776–1963", Simon and Schuster: New York, 2019. (gBooks, worldcat)

But the more sober account was this:

As the days and weeks trickled by, McCarthy seemed ever more demoralized, sometimes almost dazed, often di­sheveled, wandering aimlessly about Washington, Capitol Hill, or Wisconsin, enduring a sort of silent treatment from once-deferential senators, checking in and out of the hospital (usually to dry out), ignoring all urgings* that he stop drink­ing — a stubbly-bearded, foul-breathed shadow of the much-feared inquisitor of 1953 and 1954, a shabby remnant of the man who had tormented two presidents.

*: Including those of doctors, senators, and, repeatedly, Jean Kerr McCarthy, who nevertheless, in later years, always denied that her husband had had a drinking problem.

— Tom Wicker: "Shooting Star. The Brief Arc of Joe McCarthy", Harcourt: Orlando, Austin, 2006, p185. worldcat

One noting McCarthy's apparent refusal to see any visitors in his final days:

On April 28 he entered Bethesda for the last time. He was placed in a guarded room on the twelfth floor and allowed but one visitor, his wife, who gamely told reporters that Joe had a knee problem, nothing more. But Drew Pearson, who had contacts inside the hospital, wrote in his diary that “Senator McCarthy has been drinking heavily. … He is in an oxygen tent and has delirium tremens.”

By coincidence, Senator Prescott Bush was in Bethesda for a physical examination. He tried to visit Joe, without success, and eventually sent him a note through one of the floor nurses. “When I got back to my office,” Bush recalled, “… I found a telephone message dictated by McCarthy … in which he thanked me very warmly for coming to see him, and he couldn’t tell me how much he appreciated that.”

Joe died the following day — May 2, 1957 — with his wife and a priest at his bedside. The official cause of death was listed as acute hepatitis — or inflammation of the liver. There was no mention of cirrhosis or delir­ium tremens, though the press hinted, correctly, that he drank himself to death.

— David M. Oshinsky: "A Conspiracy So Immense. The World of Joe McCarthy", Free Press: New York, London, 1983, p505. worldcat

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